| Commit message (Collapse) | Author | Age | Files | Lines |
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h5diff issues "unable to read attribute" error message when comparing two files
Description:
h5diff did not handle attributes of variable length strings correctly. It created the wrong memory type if one but not both compared attributes are of the variable strings type. It ended in H5Aread() failure.
Solution:
We decided to treat the case when one type is variable length string and the other is not as incomparable. That bypassed the above error. We still need to figure out the proper way, if possible, to compare variable string with non-variable string types.
Tested: h5committested plus tested in Swallow (OS X 10.8).
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HDFFV-7643 - h5diff - incorrect exit-code returns for extra attribute exist
Description:
h5diff: Fixed to return correct exit code 1 when detect unique
attribute. Prior to this fix, h5diff returned exit code 0 indicating
two files are identical.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), fred (mac64-LE), emu (solaris-BE), Windows (32-LE cmake), cmake (jam)
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HDFFV-5919 - GMQS: h5diff - The number of object difference is not consistent between dataset and group/type when attribute(s) have differences
Description:
Object differences are not consistent between dataset and group/datatype when their attribute(s) have differences. This is because attribute(s) differences is not accumulated to group or datatype object’s difference, but accumulated to dataset difference.
To fix, do not accumulate attribute difference to dataset difference. This is referred to h5diff’s default behavior and also past report from users that users were confused by the accumulated behavior. (also can’t figure out only for dataset difference , also hard to spot dataset difference when it has lots of attributes or differences)
This also lead to fix inconsistent format indicating difference between dataset and group/datatype object.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), cmake (jam)
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Address HDFFV-7942 - h5diff: incorrect result for comparing attribute data with different type size in same class
Description:
When comparing attribute data values with same type class but different size, the result was incorrect. It was due to the size difference and got truncated.
Fixed to match up the smaller type size to big type size like what dataset does.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), cmake (jam)
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Fix for HDFFV-7998-h5diff: incorrect behavior and output for comparing symbolic dangling links without following-symlinks option
Description:
Fix not to check and display dangling link status without --follow-symlinks option.
Berfor the fix, when comparing symbolic link to symbolic link without follow-symlinks option, h5diff followed to check if those links are dangling or not. It caused to display output incorrectly (dangling link instead of symbolic link).
The fix also improved performance when comparing lots of symbolic links without the --follow-symlinks option.
Test cases were added and tagged with jira#.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
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Fix for HDFFV-7644 GMQS: h5diff - incorrect behaviors when comparing HDF5 files with different type of objects (dataset, group, type) as common objects
Description:
Fixed failure for comparing same named object with different object types in comparing groups. (common object comparison)
Prior to the fix, h5diff resulted in error. After the fix, h5diff detects such case as non-comparable and display messages accordingly.
Test cases were added and tagged with jira#.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
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non-executable files.
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Fix for HDFFV-7837 - h5diff: incorrect behavior with exclude-path option when unique object exist only in one file
Description:
If unique objects exists only in one file and try to exclude
the unique objects with --exclude-path option, h5diff missed
excluding some objects.
Fixed to exclude objects correctly in such case.
Test cases were added and tagged with jira#.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
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Fix for HDFFV-7835 h5diff: incorrect result for comparing the two same type symlinks as dangling links.
Description:
When two symbolic dangling links are compared with --follow-symlinks option,
the result should be same. It works for comparing two files, but didn't work
for comparing two objects.
Test cases were added and tagged with jira#.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
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Fix for HDFFV-7836 h5diff: displays error stack message for comparing the two dangling symlink with follow-symlinks option
Description:
While ago, to improve performance, skipping same object checking
(h5tools_is_obj_same()) was added.
However the checking function doesn't understand about the dangling link and
caused the issue.
Since handling dangling link code section already implemented, move the
checking function after handling dangling-links to address the problem.
Test was added and tagged with jira#.
Tested:
jam (linux32-LE), koala (linux64-LE), ostrich (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE cmake), Cmake (jam)
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HDFFV-7770 - h5diff segmentation fault on JPSS files
Description:
Fixed segfault over non-comparable attribute with different dimention or
rank, along with '-c' option to display details.
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows, Cmake
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HDFFV-7693 - h5diff produces different behavior between versions: 1.8.3 and 1.8.6
Description:
There were two issues on this.
One was not displaying all the comparable objects if non-comparable
object/attribute exist and compared before comparables ones. This issue
occurred after 1.8.4 release. This is the issue from user.
The other issue was not displaying all the comparable attributes,
if non-comparable object/attribute exist and compared ahead. This issue
were exist even before 1.8.4 release. So it's possible some attribute
comparison may have not displayed correctly in the past, if non-comparable
data were exist in common object.
Fixed h5diff to display all the comparable object and attribute regardless
of non-comparables.
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam, Windows)
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HDFFV-7712 - h5diff: segfault over combinations of complex container types (compound, array, vlen)
Description:
- Fixed segfault over dataset with container types (array,lven) with multiple nested compound types. (ex: compound->array->compound, compound->vlen->compound)
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam)
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Add test cases for HDFFV-7656 - "--delta=something" considers two NaN of the same type are different.
The fix was added (r21105) before but test cases were incorrectly added and missing for cmake script.
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), cmake
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- h5repack: h5repack failed to copy dataset if the layout is changed from chunked with
unlimited dims to contiguous. (PC -- 2011/07/15)
- h5diff: "--delta" option considers two NaN of the same type are different, which is wrong
based on http://www.hdfgroup.org/HDF5/doc/RM/Tools.html#Tools-Diff. (PC -- 2011/07/15)
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Work for HDFFV-7600 - GMQS: h5diff - argument options -d, -p and --use-system-epsilon should be mutually exclusive.
Description:
Fixed h5diff to display instructive error message and exit with 1
when mutually exclusive options (-d, -p and --use-system-epsilon)
are used together.
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Cmake (jam)
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H5Dread() produces different output for invalid enum type values
on systems of different endiannes. On BE systems, it always
emits -1. On LE systems, the invalid value is emitted. This
difference caused the h5diff test to fail since it tests to
see if different invalid enum values are reported as different
(on BE systems they are not since -1 == -1).
This fix removes the "invalid vs. different invalid" test
while we fix the library bug. HDFFV-7527 will be reopened
in JIRA until the full test passes.
Tested on: jam, heiwa, linew
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not represent a valid enum value.
Description:
The h5diff code compares enum values by converting them to strings and
then comparing them. When the enum value is out of range and can't be
converted to an enum string representation, the comparison was skipped.
The code now flags differences when one of the two enum values is out
of range (two out of range values are compared in memory). A test has
been added to the tools test script.
This fixes JIRA HDFFV-7527
Tested on: jam, koala, heiwa (h5committest)
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- HDFFV-5928 - GMQS: h5diff problem and improvement on comparsing the same objects
Description:
Fixed:
1) adding h5tools_is_obj_same() function to check if two given IDs or paths point to the same object. This function can be very useful for other tools and applications.
2) using h5tools_is_obj_same() at h5diff() and diff() in h5diff.c. If two paths point to the same object, there is no need to check the details of the object since we know there is no difference. The fix will increase the performance by skipping the content comparison. It also fixed the problem of reporting difference for some cases of comparing the same file, e.g. empty files or files with incomparable objects the same file.
Test update:
Updat prvious test cases (171, 172, 530) affected by this fix, so they
still perfrom originally intended testing without bypassing.
Tested:
jam (linux32-LE), koala (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), cmake
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check in these 2 data files for the test.
Now test is needed.
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cases in the tests for h5dump and h5diff. I also added the
test cases in the CMAKE script.
Tested on jam, linew, and amani. Tested CMAKE on jam.
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Fixed Bug 2184 - GMQS: h5diff - incorrect calculation code for
--use-system-epsilon option
Description:
Additional check in from the previous checkin r20424.
Updated help page again.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
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Fixed Bug 2184 - GMQS: h5diff - incorrect calculation code for
--use-system-epsilon option
Description:
Additional check in from the previous checkin r20384.
Updated help page.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
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Fixed Bug 2184 - GMQS: h5diff - incorrect calculation code for
--use-system-epsilon option
Description:
Merged from HDF5 1.8 branch r20369.
Fixed h5diff for --use-system-epsilon option: the calculation changed
from ( |a - b| / b ) to ( |a - b| ). This was decided for better
performance and was corrected only in HDF5 trunk, so 1.8 got updated.
Also comments for equal_XXX() function were updated correctly.
Also help page and RM got updated correctly.
Also add test cases for testing the differences w/wo the option.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE), Windows (32-LE)
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Fixed CHICAGO: Bug 2121 - h5diff - incorrect and lack of output for the
different set of attributes (different number and names)
Description:
This is related to previous checkin r20294.
Add help page update for verbose option level feature, which displays
useful information about attribute difference with -v1, --verbose=1 -v2
or --verbose=2 option.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
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Fixed CHICAGO: Bug 2121 - h5diff - incorrect and lack of output for the
different set of attributes (different number and names)
Description:
Previously h5diff compared attributes correctly only when two objects have
the same number of attributes and attribute names are identical.
This fix covers all other cases.
Also didn't display useful information about attribute difference.
This fixes both issues.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
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Bug 2089 - GMQS: h5diff segfault on a compound dataset with fixed length +
vlen string type order
Description:
This is fix for the segfault when h5diff compares a compound dataset with
combination of fixed length string types and vlen string types in certain
orders. Optimized vlariable length string handling codes. The fix is
referred from h5dump handling vlen strings.
For testing, several compound datasets were added with various combinations.
Previous failed cases:
- Vlen string, Fixed length string, Vlen string, Fixed length string
- Fixed length string, Fixed length string, Vlen string, Vlen string
- Fixed length string, Vlen string, Fixed length string, Vlen string
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (mac32-LE), linew (solaris-BE)
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Fixed h5diff to handle variable-length strings in a compound dataset
correctly. Also variable-length string array in a compound dataset.
Bug #1989.
Description:
Garbage values were displayed when h5diff compared variable-length
strings (or string array) in a compound type dataset.
Tested:
jam (linux32-LE), amani (linux64-LE), heiwa (linuxppc64-BE), tejeda (Mac32)
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Update help page for exclude-path feature.
Description:
Related to "1890: h5diff excluding object for file comparison via command line" checkins. (r19406)
Tested:
jam, amani, heiwa
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Fix for group comparison with exclude-path case. Use relative path.
Description:
Related to "1890: h5diff excluding object for file comparison via command line" checkins. (r19406)
Tested:
jam, amani and heiwa
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Add missing files from the previous checkin.
(Add extra test cases for Bug1975 h5diff - support recursive comparison on group when specified as an object)
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Add extra test cases for bug1975 h5diff - support recursive comparison on group when specified as an object.
Description:
Additional tests for combination of group recursive and --follow-symlinks
with multi-linked external links with several files (same name/strucure).
Tested:
jam, amani, heiwa
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Add --exclude-path option
Description:
Specified path to an object will be excluded from comparing the two files or two groups. If group is specified all the member objects will be excluded.
Related to "1890: h5diff excluding object for file comparison via command line"
Tested:
jam, amani and heiwa
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Fix for Bug1975 h5diff - support recursive comparison on group when specified as an object
Description:
Compare member objects and groups recursively when two files or groups are specified to be compared. Support parallel diff and handling symbolic links accordingly.
Tested:
jam, amani, heiwa
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Rename '--follow-links' to '--follow-symlinks'
Description:
The '--follow-links' option is to follow symbolic links (soft and external).
Make the name more intuitive and specific to the feature.
Tested:
jam, amani and linew
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Tested: Local linux
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629 file exit code
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bugzilla 1754: h5diff: support comparing through links.
Description:
Fix incorrect (or hanging) behavior in parallel mode when specifying
invalid combination of command options.
(ex: -v and -q , --no-dangling-links without --follow-links)
Add relate test case
Update h5diffgentest.c due to add test files this and previous time
Note:
svn #18266 (prior to this)
svn #18164 (original check-in)
Tested:
h5committest (jam, amani and linew)
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bugzilla 1754: h5diff: support comparing through links.
(original check-in svn revision #18164)
Description:
fix the hang issue in parallel mode when compare external-link.
add --no-dangling-links option.
add test cases (#450-#459) relate to the new option.
improve test script to check exit code.
update --help relate to the new options.
correct some indentations.
Tested:
h5committest (jam, amani and linew)
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Take care of test case fail for h5repack from checkin (r18164)
Description:
Previous checkin didn't allow h5diff to return succeed when a link's
target object doesn't exist. Changed it to succeed with warning.
(Need to discuss related feature)
Tested on Jam
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Add test cases for h5diff check-in (svn revision #18164).
Description:
This test cases are for testing comparing through various link combinations
relate to bugzilla report 1754.
Also improved the test script to handle external link cases and
simplified to use single line instead of double for each test cases.
Tested on Jam
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Additional fix relted to the fix of bug1672.
Description:
The fix of bug1672 caused some changes of output which required modifying
some test cases. After some discussion, restoring the changes of the test
cases was decided. After many experiments for the solution, this fix was
made so the code which improved performance can stay.
Tested on Jam.
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Add test case relate to bug1749. Also corrected command echo lines which
don't match with actual tests.
Tested on Jam.
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Fix Bug1672 - Display garbage value on LE machine for BE data.
Description:
Casuing by calling diff_dataset twice when -r or no option was given.
Change to call it once which fix the problem.
It also improves the performance. (diffing time in half)
According further test, it also occurred on BE machine as well and it
seems occruing only with the BE data attached to Bugzilla.
Don't know how the file was created. Anyway this fix will prevent
from diffing with garbage values in similiar potential case.
Tested on:
linux32 (jam) , linux64 (almani), solaris (linew)
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" Use "--use-system-epsilon" for system EPSILON
" Use "-p" or "-d" for whatever user's choice of epsilon
" Use "-p 0" or "-d 0" for strict equality (same as default)
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Added test cases
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tested: windows, linux
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the case of different classes
tested: windows, linux
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